On Dec 9, 2007, at 3:02 AM, Prof Brian Ripley wrote: > The fix is to install source packages: use argument type="source", > including AFAICS as an argument to biocLite(). Or set > options(pkgType="source"). > > Simon: it is unclear to me what build this is, but could the default > not be pkgType="source" for off-CRAN builds? I don't think we > should be expecting third parties to support architectures the CRAN > build does not. >
It is the "experimental" Leopard quad-arch nightly build and yes, changing the default package type is a good idea. I'll look into this. Thanks, Simon > > On Sun, 9 Dec 2007, Á¤ ÅÂÈÆ wrote: > >> The binaries in http://r.research.att.com/ worked great! >> Thanks a lot for the tip. >> >> However, when I tried to install bioconductor libraries using >> biocLite, I got the following error message: >> >> bash-3.2$ R --arch=x86_64 >> >> R version 2.6.1 Patched (2007-12-06 r43615) >> Copyright (C) 2007 The R Foundation for Statistical Computing >> ISBN 3-900051-07-0 >> >> R is free software and comes with ABSOLUTELY NO WARRANTY. >> You are welcome to redistribute it under certain conditions. >> Type 'license()' or 'licence()' for distribution details. >> >> R is a collaborative project with many contributors. >> Type 'contributors()' for more information and >> 'citation()' on how to cite R or R packages in publications. >> >> Type 'demo()' for some demos, 'help()' for on-line help, or >> 'help.start()' for an HTML browser interface to help. >> Type 'q()' to quit R. >> >> > source("http://www.bioconductor.org/biocLite.R") >> > biocLite(lib="~/Library/R64") >> Running biocinstall version 2.1.8 with R version 2.6.1 >> Your version of R requires version 2.1 of Bioconductor. >> Will install the following packages: >> [1] "affy" "affydata" "affyPLM" "annaffy" >> "annotate" >> [6] "Biobase" "Biostrings" "DynDoc" "gcrma" >> "genefilter" >> [11] "geneplotter" "hgu95av2" "limma" "marray" >> "matchprobes" >> [16] "multtest" "ROC" "vsn" "xtable" >> "affyQCReport" >> Please wait... >> >> trying URL >> 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/affy_1.16.0.tgz' >> Content type 'application/x-gzip' length 1683130 bytes (1.6 Mb) >> opened URL >> ================================================== >> downloaded 1.6 Mb >> >> ... < skip > ... >> >> trying URL >> 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/affyQCReport_1.16.0.tgz' >> Content type 'application/x-gzip' length 145478 bytes (142 Kb) >> opened URL >> ================================================== >> downloaded 142 Kb >> >> >> The downloaded packages are in >> /var/folders/T0/T0X1+9S9ExGTArjMjd98hk+++TI/-Tmp-//Rtmp90AT9K/ >> downloaded_packages >> > library(affy, lib="~/Library/R64") >> Error: package 'affy' is not installed for 'arch=x86_64' >> >> Is there any special way to install any packages for 64-bit >> compatible >> manner? >> >> Thanks in advance, >> >> 2007. 12. 08, ¿ÀÀü 2:11, Simon Urbanek ÀÛ¼º: >> >>> >>> On Dec 6, 2007, at 9:40 PM, Á¤ ÅÂÈÆ wrote: >>> >>>> Hi, All; >>>> >>>> I've compiled and installed successfully "presumably" 64-bit R on >>>> Leopard. >>>> But when I tried to run R, I got the following error: >>>> >>>> /usr/bin/R: line 179: /Library/Frameworks/R.framework/Resources/ >>>> etc/ >>>> i386/ldpaths: No such file or directory >>>> >>> >>> I'm pretty sure that your /usr/bin/R comes from a different build. >>> Make sure you remove old scripts. >>> >>> FWIW: dual 32-bit and 64-bit binaries of current R 2.6.1 patched and >>> R-devel for Leopard are available from >>> http://r.research.att.com/ >>> They support all four architectures. To start 64-bit Intel R use R >>> -- >>> arch=x86_64, for 64-bit ppc it is R --arch=ppc64. >>> >>> Cheers, >>> Simon >>> >>> >>>> Here is the configuration I used: >>>> >>>> CONFIG_SHELL=/bin/bash ../R-devel/configure r_arch=x86_64 >>>> LDFLAGS="- >>>> L/ >>>> usr/local/lib64 -L/usr/X11R6/lib" CC='gcc-4.2 -g -O3' CXX='g+ >>>> +-4.2 - >>>> g - >>>> O3' F77='gfortran -g -O3' FC='gfortran -g -O3' --with-blas='- >>>> framework >>>> vecLib' --with-lapack >>>> >>>> Thanks in advance >>>> >>>> Tae-Hoon Chung >>>> >>>> Korea Centers for Disease Control & Prevention (KCDC) >>>> Korea National Institute of Health (KNIH) >>>> Center for Genome Sciences, Biobank for Health Sciences >>>> >>>> 194 Tongil-ro, Eunpyoung-gu, Seoul, 122-701, Korea >>>> >>>> Tel 82-2-380-2252 >>>> Fax 82-2-354-1078 >>>> Mobile 82-10-8011-1036 >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac@stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> >>>> >>> >> >> Tae-Hoon Chung >> >> Korea Centers for Disease Control & Prevention (KCDC) >> Korea National Institute of Health (KNIH) >> Center for Genome Sciences, Biobank for Health Sciences >> >> 194 Tongil-ro, Eunpyoung-gu, Seoul, 122-701, Korea >> >> Tel 82-2-380-2252 >> Fax 82-2-354-1078 >> Mobile 82-10-8011-1036 >> >> _______________________________________________ >> R-SIG-Mac mailing list >> R-SIG-Mac@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >> > > -- > Brian D. Ripley, [EMAIL PROTECTED] > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UK Fax: +44 1865 272595 _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac